Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with cyanide

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue

Kostan, J.Sjoeblom, B.Maixner, F.Mlynek, G.Furtmueller, P.G.Obinger, C.Wagner, M.Daims, H.Djinovic-Carugo, K.

(2010) J Struct Biol 172: 331-342

  • DOI: https://doi.org/10.1016/j.jsb.2010.06.014
  • Primary Citation of Related Structures:  
    3NN1, 3NN2, 3NN3, 3NN4

  • PubMed Abstract: 

    Chlorite dismutase (Cld) is a unique heme enzyme which transforms chlorite to chloride and molecular oxygen (reaction: ClO(2)(-)→Cl(-)+O(2)). Since bacteria with Cld play significant roles in the bioremediation of industrially contaminated sites and also in wastewater treatment, it is of high interest to understand the molecular mechanism of chlorite detoxification. Here we investigate a highly active Cld from Candidatus Nitrospira defluvii (NdCld), a key nitrifier in biological wastewater treatment, using a comprehensive structural, biochemical and bioinformatics approach. We determined the crystal structure of Cld from Candidatus Nitrospira defluvii and showed that functional NdCld is a homopentamer possessing a fold found in other Clds and Cld-like enzymes. To investigate the Cld function in more detail, site-directed mutagenesis of a catalytically important residue (Arg173) was performed and two enzyme mutants were structurally and biochemically characterized. Arginine 173 is demonstrated to play a key role in (i) controlling of ligand and substrate access and binding and (ii) in chlorite dismutation reaction. The flexible residue modulates the electrostatic potential and size of the active site entrance and might be involved in keeping transiently formed hypochlorite in place for final molecular oxygen and chloride formation. Furthermore, using a structure-based sequence alignment, we show that the residue corresponding to Arg173 is conserved in all known active forms of Cld and propose it as a marker for Cld activity in yet uncharacterized Cld-like proteins. Finally, our analysis indicates that all Clds and Cld-like enzymes employ a non-covalently bound heme as a cofactor.

  • Organizational Affiliation

    Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorite dismutase
A, B, C, D, E
241Nitrospira defluviiMutation(s): 0 
Find proteins for B3U4H7 (Nitrospira defluvii)
Explore B3U4H7 
Go to UniProtKB:  B3U4H7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3U4H7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
F [auth A],
HA [auth D],
P [auth B],
PA [auth E],
Z [auth C]
C34 H32 Fe N4 O4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
G [auth A]
H [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
G [auth A],
H [auth A],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
LA [auth D],
Q [auth B],
QA [auth E],
R [auth B],
RA [auth E],
S [auth B],
T [auth B]
O4 P
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
GA [auth C]
M [auth A]
N [auth A]
EA [auth C],
FA [auth C],
GA [auth C],
M [auth A],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
TA [auth E],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
C3 H8 O3
Query on CYN

Download Ideal Coordinates CCD File 
DA [auth C],
L [auth A],
MA [auth D],
SA [auth E],
U [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.49α = 90
b = 145.49β = 90
c = 136.011γ = 120
Software Package:
Software NamePurpose
DNAdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description